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A foothill yellow-legged frog is swabbed to check for fungus in the Sunol Regional Wilderness on Wednesday, April 8, 2015, in Sunol, Calif. Biologists are conducting weekly surveys of the frog population in the creek and are concerned about a San Francisco Public Utilities Commission plan to alter the creek bed to improve odds that steelhead trout will migrate up the creek. (Aric Crabb/Bay Area News Group)

A foothill yellow-legged frog is photographed in Alameda Creek in the Sunol Regional Wilderness on Wednesday, April 8, 2015, in Sunol, Calif. Biologists are conducting weekly surveys of the frog population in the creek and are concerned about a San Francisco Public Utilities Commission plan to alter the creek bed to improve odds that steelhead trout will migrate up the creek. (Aric Crabb/Bay Area News Group)

A foothill yellow-legged frog is photographed in Alameda Creek in the Sunol Regional Wilderness on Wednesday, April 8, 2015, in Sunol, Calif. Biologists are conducting weekly surveys of the frog population in the creek and are concerned about a San Francisco Public Utilities Commission plan to alter the creek bed to improve odds that steelhead trout will migrate up the creek. (Aric Crabb/Bay Area News Group)

A foothill yellow-legged frog is photographed in Alameda Creek in the Sunol Regional Wilderness on Wednesday, April 8, 2015, in Sunol, Calif. Biologists are conducting weekly surveys of the frog population in the creek and are concerned about a San Francisco Public Utilities Commission plan to alter the creek bed to improve odds that steelhead trout will migrate up the creek. (Aric Crabb/Bay Area News Group)

A foothill yellow-legged frog is photographed in Alameda Creek in the Sunol Regional Wilderness on Wednesday, April 8, 2015, in Sunol, Calif. Biologists are conducting weekly surveys of the frog population in the creek and are concerned about a San Francisco Public Utilities Commission plan to alter the creek bed to improve odds that steelhead trout will migrate up the creek. (Aric Crabb/Bay Area News Group)

A male foothill yellow-legged frog tries to mate with a bullfrog along Alameda Creek in the Sunol Regional Wilderness on Wednesday, April 8, 2015, in Sunol, Calif. Biologists are conducting weekly surveys of the frog population in the creek and are concerned about a San Francisco Public Utilities Commission plan to alter the creek bed to improve odds that steelhead trout will migrate up the creek. (Aric Crabb/Bay Area News Group)

SUNOL — It’s billed as a straight path to help threatened steelhead trout: Open a passageway over barriers in a boulder-lined major creek for the fish to swim upstream to spawn.

San Francisco’s water department agreed to try it for $1 million, but the plan is hitting barriers of its own. Critics say they fear the project to help the fish will hurt native frogs, including one threatened species and another one being considered for protections, in an area called Little Yosemite in Sunol Regional Wilderness.

Faster than a frog can hop over a drought-shrunken creek, San Francisco water officials’ plan to help restore wild fish has spiraled into a regulatory debate highlighting the difficulty of trying to undo damage to one species without hurting others.

Water officials had hoped to have the project done by now on Alameda Creek at Little Yosemite below where the city water department diverts creek water for its Calaveras Reservoir.

Now, the San Francisco Public Utilities Commission is waiting for a complicated, postponed hearing at the San Francisco Planning Commission on how the project is reviewed.

The East Bay Regional Park District, state Department of Fish and Wildlife, the Sierra Club, Save the Frogs and the Alameda Creek Alliance have each filed written appeals protesting San Francisco’s request for permission to permit the project without doing a full-blown environmental-impact report to consider the effects on other species.

“We have to manage to protect multiple species, not just one that is popular,” said Steve Bobzien, the East Bay park district’s ecological services coordinator. “The data shows it’s likely there will be adverse effects on frogs and amphibians from this project, and that it is unlikely that even a few (steelhead) will even make it up the creek in most years.”

At risk, the five organizations say, is the threatened California red-legged frog and the foothill yellow-legged frog, a rare species for which environmentalists are seeking protection.

The groups worry that tinkering with the natural streambed will introduce predators and disease that can decimate local frog populations, and harm water conditions that make the Little Yosemite area a rich enclave for frogs.

Steelhead restoration projects have raised concerns about frogs on other creeks in California, said Jeff Miller, executive director for the Alameda Creek Alliance. West Coast steelhead populations have declined sharply because of dams, barriers, water diversions, habitat loss, overfishing, pollution and erosion from logging.

“We want the steelhead to make it to the upper stretches of the creek,” Miller said, “but we think the Little Yosemite project was not well thought out, and should be reconsidered.”

The Sierra Club said it was disturbed by the water department’s “seriously flawed” conclusion that the project will have no significant environmental impacts.

The project would line parts of the creek bed with concrete and plug gaps between some boulders to create deeper, longer pools for steelhead to pick up momentum and leap into higher pools.

The work would be done along a 0.4-mile-long stretch of creek.

Critics say opening up the creek flows will allow bullfrogs and crayfish to move upstream to prey on frogs and frog eggs in Little Yosemite, and make the area more vulnerable to the chytrid fungus that is killing frogs worldwide.

“They want to make it more like a swimming pool, but that will change everything about the depth, flows and hydrology that makes this such a valuable place for the frogs,” said Sarah Kupferberg, a scientist who has studied Alameda Creek frogs.

Drought has exacerbated the concerns, making Little Yosemite an especially important stronghold for the frogs, she said.

In a frog survey in spring, Kupferberg and Bobzien discovered a bullfrog had made it much further upstream into Little Yosemite than ever documented before.

For their part, San Francisco water officials said they believe they can help the majestic steelhead — a species that weighs up to 45 pounds and lives in oceans and return to creeks to spawn — without harming the local frogs.

“We appreciate these concerns, but we simply have a difference of opinion about the impacts of the fish-passage project,” said Tim Ramirez, San Francisco PUC’s director of natural resources and land management. “We are not building a dam on the creek.”

The stream alterations will be as modest as possible, and not mar the scenery of the popular area with a series of pools, Ramirez said.

Steelhead and foothill yellow-legged frogs have coexisted in other California creeks, he added.

San Francisco water officials were required to propose the Little Yosemite fish-passage project as a condition of winning approval from the National Marine Fishery Service for the SFPUC’s seismic rebuild of the Calaveras Reservoir dam further upstream.

“We take our commitments seriously,” Ramirez said.

Miller said that before seeking permits for the project, San Francisco should wait until other fish-passage projects on lower Alameda Creek near Fremont have been done and evaluated to determine whether steelhead were helped.